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- PDB-1ims: MOLECULAR STRUCTURE OF THE HALOGENATED ANTI-CANCER DRUG IODODOXOR... -

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Basic information

Entry
Database: PDB / ID: 1ims
TitleMOLECULAR STRUCTURE OF THE HALOGENATED ANTI-CANCER DRUG IODODOXORUBICIN COMPLEXED WITH D(TGTACA) AND D(CGATCG)
ComponentsDNA (5'-D(*CP*GP*AP*TP*CP*G)-3')
KeywordsDNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG
Function / homology4'-DEOXY-4'-IODODOXORUBICIN / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsBerger, I. / Su, L. / Spitzner, J.R. / Kang, C. / Burke, T.G. / Rich, A.
CitationJournal: Nucleic Acids Res. / Year: 1995
Title: Molecular structure of the halogenated anti-cancer drug iododoxorubicin complexed with d(TGTACA) and d(CGATCG).
Authors: Berger, I. / Su, L. / Spitzner, J.R. / Kang, C. / Burke, T.G. / Rich, A.
History
DepositionOct 23, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0Apr 4, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*AP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,4642
Polymers1,8091
Non-polymers6541
Water93752
1
A: DNA (5'-D(*CP*GP*AP*TP*CP*G)-3')
hetero molecules

A: DNA (5'-D(*CP*GP*AP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,9274
Polymers3,6182
Non-polymers1,3092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)27.730, 27.730, 52.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: DNA chain DNA (5'-D(*CP*GP*AP*TP*CP*G)-3')


Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-DM7 / 4'-DEOXY-4'-IODODOXORUBICIN / 4'-DEOXY-4'-IODOADRIAMYCIN


Mass: 654.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H29INO10
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3SPERMINE11
4KCL11
5K CACODYLATE11
6WATER12
7MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mMspermine1drop
240 mM1dropKCl
320 mMpotassium cacodylate1drop
45 %MPD1drop
52 mMd(CGATCG)1drop
64 mMiododoxorubicin1drop
730 %1reservoir

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Data collection

DiffractionMean temperature: 277 K
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 1.5→10 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.18 -
obs0.18 3028
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 135 39 52 226
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 10 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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